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- PDB-4mj9: lambda-[Ru(TAP)2(dppz-10-Me)]2+ bound to a synthetic DNA oligomer -

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Basic information

Entry
Database: PDB / ID: 4mj9
Titlelambda-[Ru(TAP)2(dppz-10-Me)]2+ bound to a synthetic DNA oligomer
ComponentsDNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
KeywordsDNA / methyl-substituted / Intercalation / Ruthenium / asymmetric substitution
Function / homologyChem-2J0 / : / DNA
Function and homology information
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.97 Å
AuthorsHall, J.P. / Cardin, C.J.
CitationJournal: Organometallics / Year: 2015
Title: The Structural Effect of Methyl Substitution on the Binding of Polypyridyl Ru dppz Complexes to DNA
Authors: Hall, J.P. / Beer, H. / Buchner, K. / Cardin, D.J. / Cardin, C.J.
History
DepositionSep 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 18, 2015Group: Database references
Revision 1.2May 13, 2015Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,9814
Polymers3,0461
Non-polymers9353
Water2,090116
1
A: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules

A: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)7,9618
Polymers6,0922
Non-polymers1,8696
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_556y,x,-z+11
Buried area760 Å2
ΔGint-4 kcal/mol
Surface area4260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.270, 42.270, 39.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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Components

#1: DNA chain DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')


Mass: 3045.992 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: DNA synthesised by ATDBio
#2: Chemical ChemComp-2J0 / (10-methyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+)


Mass: 761.758 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H24N12Ru
#3: Chemical ChemComp-BA / BARIUM ION


Mass: 137.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ba
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 1ul 1mM d(TCGGCGCCGA)2, 1ul 4mM rac-Ru(TAP)2(dppz-10-Me)]2+, 6ul 40mM Na cacodylate pH 6.3, 12mM spermine-tetra HCl, 20mM BaCl2, 80mM KCl, 10% 2-methyl-2,4-pentanediol equilibriated against ...Details: 1ul 1mM d(TCGGCGCCGA)2, 1ul 4mM rac-Ru(TAP)2(dppz-10-Me)]2+, 6ul 40mM Na cacodylate pH 6.3, 12mM spermine-tetra HCl, 20mM BaCl2, 80mM KCl, 10% 2-methyl-2,4-pentanediol equilibriated against 1ml 35% 2-methyl-2,4-pentanediol , VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.8856 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 12, 2013
RadiationMonochromator: dual Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 0.97→21.14 Å / Num. all: 20804 / Num. obs: 20804 / % possible obs: 95.9 % / Observed criterion σ(I): 2.6
Reflection shellResolution: 0.97→1 Å / % possible all: 98.7

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Processing

Software
NameVersionClassification
GDAdata collection
SHELXCDphasing
SHELXEmodel building
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: SAD / Resolution: 0.97→21.14 Å / Cor.coef. Fo:Fc: 0.991 / Cor.coef. Fo:Fc free: 0.989 / SU B: 0.328 / SU ML: 0.008 / Cross valid method: THROUGHOUT / ESU R: 0.013 / ESU R Free: 0.013 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.09564 1069 5.1 %RANDOM
Rwork0.08601 ---
obs0.0865 19713 94.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.357 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å2-0 Å2-0 Å2
2---0.14 Å2-0 Å2
3---0.28 Å2
Refinement stepCycle: LAST / Resolution: 0.97→21.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms0 202 54 116 372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0320.013291
X-RAY DIFFRACTIONr_bond_other_d0.0020.02137
X-RAY DIFFRACTIONr_angle_refined_deg2.5491.604458
X-RAY DIFFRACTIONr_angle_other_deg1.4283313
X-RAY DIFFRACTIONr_dihedral_angle_1_deg
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.230
X-RAY DIFFRACTIONr_gen_planes_refined0.0310.02177
X-RAY DIFFRACTIONr_gen_planes_other0.0060.0277
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.2731.306291
X-RAY DIFFRACTIONr_scbond_other1.2711.308292
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7221.958459
X-RAY DIFFRACTIONr_long_range_B_refined4.44615.964756
X-RAY DIFFRACTIONr_long_range_B_other2.93314.934681
X-RAY DIFFRACTIONr_rigid_bond_restr2.2653427
X-RAY DIFFRACTIONr_sphericity_free45.644526
X-RAY DIFFRACTIONr_sphericity_bonded13.4295483
LS refinement shellResolution: 0.97→0.995 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.162 89 -
Rwork0.191 1475 -
obs--98.24 %

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